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geneontology / go-annotation

This repository hosts the tracker for issues pertaining to GO annotations.
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PTN002449977 THIOREDOXIN-DEPENDENT PEROXIDE REDUCTASE (PTHR42801) #4206

Closed sjm41 closed 2 years ago

sjm41 commented 2 years ago

This node is annotated with "thioredoxin peroxidase activity" (GO:0008379). But I think it should use the new term thioredoxin-dependent peroxiredoxin activity (GO:0140824) = EC:1.11.1.24

Source annotations are: PTN000841000 (ECOLI|EcoGene=EG10108|UniProtKB=P0AE52) PTN000074145 (YEAST|SGD=S000001272|UniProtKB=P40553) @srengel PTN000074148 (SCHPO|PomBase=SPBC1773.02c|UniProtKB=O94561) @ValWood PTN000074033 (DROME|FlyBase=FBgn0038519|UniProtKB=Q9VEJ0) <- I've changed this one PTN002533774 (HUMAN|HGNC=9354|UniProtKB=P30048) <- disputed in P2GO

sjm41 commented 2 years ago

related to #4205

ValWood commented 2 years ago

Does the same apply to pombe tpx1 from the same paper? or is it just bcp1/SPBC1773.02c

sjm41 commented 2 years ago

@ValWood I only mentioned the one on the PAINT node I encountered, but yes, from reading the abstract of PMID: 20356456 and checking the EC number on the UniProt entry, the same applies to tpx1. The abstract suggests the same is also true of gpx1 (though you have annotated a "NOT thioredoxin peroxidase activity" for that one?)

ValWood commented 2 years ago

OK thanks done.

sjm41 commented 2 years ago

Closing this. Turned out the real issue here is a relationship issue in the GO, compounded by ambiguous names - ticket to fix this is https://github.com/geneontology/go-ontology/issues/23121#issuecomment-1161798387

Basically, "thioredoxin peroxidase activity" (GO:0008379) is a more specific term than "thioredoxin-dependent peroxiredoxin activity (GO:0140824) = EC:1.11.1.24", so the former should be a child of the latter.

Should use "thioredoxin peroxidase activity" when substrate is specifically H2O2 and use "thioredoxin-dependent peroxiredoxin activity" when there is broader substrate specificity for any hydroperoxide (e.g. cumene hydroperoxide. text-butyl hydroperoxide, H2O2)

@ValWood The changes you made are still correct - PMID: 20356456 tested all three hydroperoxides I mentioned above.